[English] 日本語
Yorodumi
- EMDB-13765: OMCC C1 at 3.28A - Refinement without symmetry of the outer membr... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-13765
TitleOMCC C1 at 3.28A - Refinement without symmetry of the outer membrane core complex (O- and I-layer) from the fully-assembled R388 type IV secretion system.
Map dataOMCC C1 at 3.28 - 3D refinement of the Core Complex (OMCC) without symmetry using all particles - Unsharpened
Sample
  • Complex: Type IV secretion system complex
Keywordstype IV secretion system / type 4 secretion system / T4SS / OMCC / core complex / O-layer / I-layer / R388 plasmid / conjugation / bacterial secretion / secretion / secretion system / protein complex / VirB7 / VirB9 / VirB10 / TrwN / TrwF / TrwE / MEMBRANE PROTEIN
Biological speciesEscherichia coli (E. coli)
Methodsingle particle reconstruction / cryo EM / Resolution: 3.61 Å
AuthorsMace K / Vadakkepat AK / Waksman G / Lukoyanova N
Funding support United Kingdom, 4 items
OrganizationGrant numberCountry
Wellcome Trust098302 United Kingdom
Wellcome Trust217089 United Kingdom
Wellcome Trust202679/Z/16/Z United Kingdom
Wellcome Trust206166/Z/17/Z United Kingdom
CitationJournal: Nature / Year: 2022
Title: Cryo-EM structure of a type IV secretion system.
Authors: Kévin Macé / Abhinav K Vadakkepat / Adam Redzej / Natalya Lukoyanova / Clasien Oomen / Nathalie Braun / Marta Ukleja / Fang Lu / Tiago R D Costa / Elena V Orlova / David Baker / Qian Cong ...Authors: Kévin Macé / Abhinav K Vadakkepat / Adam Redzej / Natalya Lukoyanova / Clasien Oomen / Nathalie Braun / Marta Ukleja / Fang Lu / Tiago R D Costa / Elena V Orlova / David Baker / Qian Cong / Gabriel Waksman /
Abstract: Bacterial conjugation is the fundamental process of unidirectional transfer of DNAs, often plasmid DNAs, from a donor cell to a recipient cell. It is the primary means by which antibiotic resistance ...Bacterial conjugation is the fundamental process of unidirectional transfer of DNAs, often plasmid DNAs, from a donor cell to a recipient cell. It is the primary means by which antibiotic resistance genes spread among bacterial populations. In Gram-negative bacteria, conjugation is mediated by a large transport apparatus-the conjugative type IV secretion system (T4SS)-produced by the donor cell and embedded in both its outer and inner membranes. The T4SS also elaborates a long extracellular filament-the conjugative pilus-that is essential for DNA transfer. Here we present a high-resolution cryo-electron microscopy (cryo-EM) structure of a 2.8 megadalton T4SS complex composed of 92 polypeptides representing 8 of the 10 essential T4SS components involved in pilus biogenesis. We added the two remaining components to the structural model using co-evolution analysis of protein interfaces, to enable the reconstitution of the entire system including the pilus. This structure describes the exceptionally large protein-protein interaction network required to assemble the many components that constitute a T4SS and provides insights on the unique mechanism by which they elaborate pili.
History
DepositionOct 21, 2021-
Header (metadata) releaseJun 22, 2022-
Map releaseJun 22, 2022-
UpdateDec 13, 2023-
Current statusDec 13, 2023Processing site: PDBe / Status: Released

-
Structure visualization

Supplemental images

emd_13765.png

Downloads & links

-
Map

FileDownload / File: emd_13765.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationOMCC C1 at 3.28 - 3D refinement of the Core Complex (OMCC) without symmetry using all particles - Unsharpened
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.07 Å/pix.
x 300 pix.
= 320.1 Å		1.07 Å/pix.
x 300 pix.
= 320.1 Å		1.07 Å/pix.
x 300 pix.
= 320.1 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.067 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 0.25
Minimum - Maximum-0.24392574 - 0.7559397
Average (Standard dev.)0.012381777 (±0.049714584)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 320.1 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_13765_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Original Ab initio OMCC - Ab initio reconstruction...

Fileemd_13765_additional_1.map
AnnotationOriginal Ab initio OMCC - Ab initio reconstruction without symmetry from 100,000 particles
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Ab initio model for OMCC C1 - 3D...

Fileemd_13765_additional_2.map
AnnotationAb initio model for OMCC C1 - 3D refinement using original ab initio as initial model, without symmetry from 100,000 particles - Sharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Ab initio model for OMCC C1 - 3D...

Fileemd_13765_additional_3.map
AnnotationAb initio model for OMCC C1 - 3D refinement using original ab initio as initial model, without symmetry from 100,000 particles - Unsharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: OMCC C1 at 3.28 - 3D refinement of...

Fileemd_13765_additional_4.map
AnnotationOMCC C1 at 3.28 - 3D refinement of the Core Complex (OMCC) without symmetry using all particles - Sharpened
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: OMCC C1 at 3.28 - Half-A

Fileemd_13765_half_map_1.map
AnnotationOMCC C1 at 3.28 - Half-A
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: OMCC C1 at 3.28 - Half-B

Fileemd_13765_half_map_2.map
AnnotationOMCC C1 at 3.28 - Half-B
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Type IV secretion system complex

EntireName: Type IV secretion system complex
Components
  • Complex: Type IV secretion system complex

-
Supramolecule #1: Type IV secretion system complex

SupramoleculeName: Type IV secretion system complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#3
Source (natural)Organism: Escherichia coli (E. coli) / Strain: R388 plasmid
Molecular weightTheoretical: 2.808 MDa

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

BufferpH: 7.6
VitrificationCryogen name: ETHANE

-
Electron microscopy

MicroscopeFEI TITAN KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Average electron dose: 57.5 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: OTHER / Imaging mode: OTHER / Nominal defocus max: 3.0 µm / Nominal defocus min: 1.5 µm
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

-
Image processing

Startup modelType of model: OTHER / Details: CryoSPARC ab-initio
Final reconstructionResolution.type: BY AUTHOR / Resolution: 3.61 Å / Resolution method: FSC 0.143 CUT-OFF / Number images used: 349413
Initial angle assignmentType: MAXIMUM LIKELIHOOD
Final angle assignmentType: OTHER / Details: Stochastic gradient descent (SGD)

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more